Mangrove microcosms capable of removing polycyclic aromatic hydrocarbons (PAHs) and polybrominated diphenyl ethers (PBDEs) from wastewater were established under everyday tidal and non-tidal flooding regimes, along with two different mangrove species. Defining how bacterial communities change with pollutants or across treatments will contribute to understanding the microbial ecology of in situ bioremediation systems. A semi-nested PCR-DGGE (denaturing gradient gel electrophoresis) approach was employed, with known genus/species-specific primers targeting the 16S rRNA genes of Sphingomonas and Mycobacterium (related to PAH degradation) and Dehalococcoides (related to PBDE degradation). Results showed that the composition of Mycobacterium- and Dehalococcoides-like populations was critically determined by tidal regime during a medium-term (4-8 months) exposure, while that of Sphingomonas-like population, along with total bacterial community, was more dependent on sediment layer and became prominently affected by tidal regime till the end of 8-month treatment. The effect of plant species was relatively small. Canonical correspondence analysis (CCA) further revealed that Sphingomonas- and Mycobacterium-like populations were significantly associated with phenanthrene and benzo(a)pyrene, respectively, while Dehalococcoides-like population was the only group significantly related to the highest PBDE congener (BDE-209) in the mangrove microcosms. (C) 2015 Elsevier B.V. All rights reserved.